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  • D Molenaar
Article

A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways

Atashgahi, S., Hornung, B., Van Der Waals, M. J., Da Rocha, U. N., Hugenholtz, F., Nijsse, B., Molenaar, D., Van Spanning, R., Stams, A. J. M., Gerritse, J. & Smidt, H., 14 Mar 2018, In : Scientific Reports. 8, 1, p. 1-12 12 p., 4490.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Amino acid analysis using chromatography–mass spectrometry: An inter platform comparison study

Krumpochova, P., Bruyneel, B., Molenaar, D., Koukou, A., Wuhrer, M., Niessen, W. M. A. & Giera, M. A., 2015, In : Journal of Pharmaceutical and Biomedical Analysis. 114, p. 398-407

Research output: Contribution to JournalArticleAcademicpeer-review

Availability of public goods shapes the evolution of competing metabolic strategies.

Bachmann, H., Fischlechner, M., Rabbers, I., Barfa, N., Branco dos Santos, F., Molenaar, D. & Teusink, B., 2013, In : Proceedings of the National Academy of Sciences of the United States of America. 110, p. 14302-14307

Research output: Contribution to JournalArticleAcademicpeer-review

Binding proteins enhance specific uptake rate by increasing the substrate-transporter encounter rate.

Bosdriesz, E., Magnúsdóttir, S., Bruggeman, F. J., Teusink, B. & Molenaar, D., 2015, In : The FEBS Journal. 282, p. 2394-2407 12.

Research output: Contribution to JournalArticleAcademicpeer-review

Bioinformatics and systems biology: bridging the gap between heterogeneous student backgrounds

Abeln, S., Molenaar, D., Feenstra, K. A., Hoefsloot, H. C., Teusink, B. & Heringa, J., Sep 2013, In : Briefings in bioinformatics. 14, 5, p. 589-98 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Characterization of cellular composition of evolved strains of Lactococcus lactis

Price, C. J., Santos, F., Molenaar, D., Teusink, B., Poolman, B. & Kuipers, O. P., Jun 2010, In : The FEBS Journal. 277, p. 114-114

Research output: Contribution to JournalArticleAcademicpeer-review

Complete genome sequence of Lactococcus lactis subsp. Lactis KF147, a plant-associated lactic acid bacterium.

Siezen, R. J., Bayjanov, J., Renckens, B., Wels, M., van Hijum, S. A. F. T., Molenaar, D. & van Hylckama Vlieg, J. E. T., 2010, In : Journal of Bacteriology. 192, p. 2649-2650

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
170 Downloads (Pure)

Convergence in probiotic Lactobacillus gut-adaptive responses in humans and mice

Marco, M. L., de Vries, M. C., Wels, M., Molenaar, D., Mangell, P., Ahrne, S., de Vos, W. M., Vaughan, E. E. & Kleerebezem, M., 2010, In : ISME Journal. 4, p. 1481-1484

Research output: Contribution to JournalArticleAcademicpeer-review

Experimental evolution and the adjustment of metabolic strategies in lactic acid bacteria

Bachmann, H., Molenaar, D., Branco dos Santos, F. & Teusink, B., 1 Aug 2017, In : FEMS Microbiology Reviews. 41, Supp_1, p. S201-S219

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Gene expression analysis reveals a gene set discriminatory to different metals in soil.

Nota, B., Verweij, R. A., Molenaar, D., Ylstra, B., van Straalen, N. M. & Roelofs, D., 2010, In : Toxicological Sciences. 115, 1, p. 34-40

Research output: Contribution to JournalArticleAcademicpeer-review

Genome instability in Lactobacillus rhamnosus GG

Sybesma, W., Molenaar, D., Ijcken, W., Venema, K. & Kort, R., 2013, In : Applied and Environmental Microbiology. 79, p. 2233-2239

Research output: Contribution to JournalArticleAcademicpeer-review

Genome-wide transposon mutagenesis indicates that Mycobacterium marinum customizes its virulence mechanisms for survival and replication in different hosts.

Weerdenburg, E. M., Abdallah, A., Rangkuti, F., Abd El Ghany, M., Otto, T. D., Adroub, S. A., Molenaar, D., Ummels, R., Ter Veen, K., van Stempvoort, G., van der Sar, A. M., Ali, S., Langridge, G. C., Thomson, N. R., Pain, A. & Bitter, W., 2015, In : Infection and Immunity. 83, p. 1778-1788 5.

Research output: Contribution to JournalArticleAcademicpeer-review

How biochemical constraints of cellular growth shape evolutionary adaptations in metabolism

Berkhout, J., Bosdriesz, E., Nikerel, E., Molenaar, D., de Ridder, D., Teusink, B. & Bruggeman, F. J., 2013, In : Genetics. 194, 2, p. 505-512

Research output: Contribution to JournalArticleAcademicpeer-review

How fast-growing bacteria robustly tune their ribosome concentration to approximate growth-rate maximization.

Bosdriesz, E., Molenaar, D., Teusink, B. & Bruggeman, F. J., 2015, In : The FEBS Journal. 282, p. 2029-2044 10.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Involvement of the mannose phosphotransferase system of Lactobacillus plantarum WCFS1 in peroxide-stress tolerance.

Stevens, M. J., Molenaar, D., de Jong, A., de Vos, W. M. & Kleerebezem, M., 2010, In : Applied and Environmental Microbiology. 76, p. 3748-3752

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
161 Downloads (Pure)

Mixed-Culture Transcriptome Analysis Reveals the Molecular Basis of Mixed-Culture Growth in Streptococcus thermophilus and Lactobacillus bulgaricus

Sieuwerts, S., Molenaar, D., van Hijum, S. A. F. T., Beerthuyzen, M., Stevens, M. J. A., Janssen, P. W. M., Ingham, C. J., de Bok, F. A. M., de Vos, W. M. & Vlieg, J. E. T. V. H., Dec 2010, In : Applied and Environmental Microbiology. 76, 23, p. 7775-7784

Research output: Contribution to JournalArticleAcademicpeer-review

Molecular analysis of the vaginal microbiome: an alternative for the diagnosis of bacterial vaginosis?

Dols, J. A. M., Molenaar, D., Helm, J., Caspers, M. P. M., de Kat-Angelino, A., Speksnijder, A. G. C. L., Westerhoff, H. V., Richardus, J. H., Boon, M. E., Reid, G., de vries, H. J. C. & Kort, R., 2015, In : BMC Infectious Diseases.

Research output: Contribution to JournalArticleAcademicpeer-review

Naturally fermented milk from northern Senegal: Bacterial community composition and probiotic enrichment with Lactobacillus rhamnosus

Parker, M., Zobrist, S., Donahue, C., Edick, C., Mansen, K., Nadjari, M. H. Z., Heerikhuisen, M., Sybesma, W., Molenaar, D., Diallo, A. M., Milani, P. & Kort, R., 21 Sep 2018, In : Frontiers in Microbiology. 9, September, p. 1-12 12 p., 2218.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Phenotypic and genomic diversity of Lactobacillues plantarum strains isolated from various environmental niches.

Siezen, R. J., Tzeneva, V. A., Castioni, A., Wels, M., Phan, H. T. K., Rademaker, J. L. W., Starrenburg, M. J. C., Kleerebezem, M., Molenaar, D. & van Hylckama Vlieg, J. E. T., 2010, In : Environmental Microbiology. 12, 3, p. 758-773

Research output: Contribution to JournalArticleAcademicpeer-review

Physiological responses to folate overproduction in lactobacillys plantarum WCFS1.

Wegkamp, H. B. A., Mars, A. E., Faijes, M., Molenaar, D., de Vos, R. C. H., Klaus, S. M. J., Hanson, A. D., Vos, W. M. & Smid, E. J., 2010, In : Microbial Cell Factories. 9, p. 100 14 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
81 Downloads (Pure)

Protein costs do not explain evolution of metabolic strategies and regulation of ribosomal content: does protein investment explain an anaerobic bacterial Crabtree effect?

Goel, A., Eckhardt, T. H., Puri, P., de Jong, A., Santos, F., Giera, M. A., Fusetti, F., Vos, W. M., Kok, J., Poolman, B., Molenaar, D., Kuipers, O. P. & Teusink, B., 2015, In : Molecular Microbiology. 97, p. 77-92 1.

Research output: Contribution to JournalArticleAcademicpeer-review

Sigma 54 mediated control of the mannose PTS in Lactobacillus plantarum impacts on carbohydrate metabolism.

Stevens, M. J., Molenaar, D., de Jong, A., de Vos, W. M. & Kleerebezem, M., 2010, In : Microbiology. 156, p. 695-707

Research output: Contribution to JournalArticleAcademicpeer-review

Systems biology of lactic acid bacteria: For food and thought

Teusink, B. & Molenaar, D., 1 Dec 2017, In : Current Opinion in Systems Biology. 6, p. 7-13 7 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

The SOS response of Listeria monocytogenes is involved in stress resistance and mutagenesis.

van der Veen, S. ., van Schalkwijk, S., Molenaar, D., de Vos, W. M., Abee, T. & Wells-Bennik, M. H. J., 2010, In : Microbiology. 156, p. 374-384

Research output: Contribution to JournalArticleAcademicpeer-review

Training for translation between disciplines: A philosophy for life and data sciences curricula

Anton Feenstra, K., Abeln, S., Westerhuis, J. A., Brancos Dos Santos, F., Molenaar, D., Teusink, B., Hoefsloot, H. C. J. & Heringa, J., 1 Jul 2018, In : Bioinformatics. 34, 13, p. i4-i12 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Vesicle trafficking via the Spitzenkoerper during hyphal tip growth in Rhizoctonia solani

Dijksterhuis, J. & Molenaar, D., 2013, In : Antonie van Leeuwenhoek. 103, p. 921-931

Research output: Contribution to JournalArticleAcademicpeer-review

Conference contribution

Constraint-based models of microbial physiology: Surprisingly versatile

Teusink, B., Planqué, B., Molenaar, D. & Bruggeman, F., 1 Jan 2018, 10th International Conference on Simulation and Modelling in the Food and Bio-Industry 2018, FOODSIM 2018. Eurosis, p. 5-10 6 p.

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review